This is a difficult issue for me regarding religious exemption.
For people who feel that the vaccine is made from the embryos of an aborted fetus and their conscience is so burdened by abortion, I consider that a religious exemption. I believe we can sign that exemption without it pricking our own conscience.
Regarding the temple of God argument, I wonder...does this person have a regimented diet to maintain optimal health as well as exercise routine? If not, then it seems deceptive to use that argument.
This being said, a relative of mine has rheumatoid arthritis and any vaccine or antibiotics causes her RA to flare up terribly. She asked her physician to give exemption and was refused...even though the doctor agreed that the RA would reek havoc for months afterward. In this case, she appealed to her pastor who gave a religious exemption. This too feels deceptive. In her case, she has 3 young children and her husband is incapacitated by Lyme's disease so that he can hardly function. She needs to work. She cannot afford to have RA take her out.
Finally, in all this we must consider Romans 13:1-5.
Let every person be subject to the governing authorities. For there is no authority except from God, and those that exist have been instituted by God. Therefore whoever resists the authorities resists what God has appointed, and those who resist will incur judgment. For rulers are not a terror to good conduct, but to bad. Would you have no fear of the one who is in authority? Then do what is good, and you will receive his approval, for he is God’s servant for your good. But if you do wrong, be afraid, for he does not bear the sword in vain. For he is the servant of God, an avenger who carries out God’s wrath on the wrongdoer. Therefore one must be in subjection, not only to avoid God’s wrath but also for the sake of conscience.
This is a remarkable passage because the Apostle Paul was writing this under the reign of Nero.
As a pastor, follow your conscience and entrust your decision to God. If you deny the exemption and the person gets mad, you may be in for a different test. Do you trust God, even at the expense of alienation from others. Can you live with your conscience and God with the decision you make? If so, do what you believe is right.
Also, canadyjd is correct. The exemption is given by government so it is not going against government to give the exemption. But, does it go against your conscience?
May God give wisdom and peace with no second guessing.